Five Quantitative Trait Loci Control Radiation-Induced Adenoma Multiplicity in Mom1R ApcMin/+ Mice

Ionising radiation is a carcinogen capable of inducing tumours, including colorectal cancer, in both humans and animals. By backcrossing a recombinant line of ApcMin/+ mice to the inbred BALB/c mouse strain, which is unusually sensitive to radiation–induced tumour development, we obtained panels of 2Gy-irradiated and sham-irradiated N2 ApcMin/+ mice for genotyping with a genome-wide panel of microsatellites at ∼15 cM density and phenotyping by counting adenomas in the small intestine. Interval and composite interval mapping along with permutation testing identified five significant susceptibility quantitative trait loci (QTLs) responsible for radiation induced tumour multiplicity in the small intestine. These were defined as Mom (Modifier of Min) radiation-induced polyposis (Mrip1-5) on chromosome 2 (log of odds, LOD 2.8, p = 0.0003), two regions within chromosome 5 (LOD 5.2, p<0.00001, 6.2, p<0.00001) and two regions within chromosome 16 respectively (LOD 4.1, p  = 4×10−5, 4.8, p<0.00001). Suggestive QTLs were found for sham-irradiated mice on chromosomes 3, 6 and 13 (LOD 1.7, 1.5 and 2.0 respectively; p<0.005). Genes containing BALB/c specific non-synonymous polymorphisms were identified within Mrip regions and prediction programming used to locate potentially functional polymorphisms. Our study locates the QTL regions responsible for increased radiation-induced intestinal tumorigenesis in ApcMin/+ mice and identifies candidate genes with predicted functional polymorphisms that are involved in spindle checkpoint and chromosomal stability (Bub1b, Casc5, and Bub1), DNA repair (Recc1 and Prkdc) or inflammation (Duox2, Itgb2l and Cxcl5). Our study demonstrates use of in silico analysis in candidate gene identification as a way of reducing large-scale backcross breeding programmes

The LRS profile of <i>Mrip4</i> and <i>Mrip5</i> against markers distributed along chromosome 16 is determined using CIM (composite interval mapping) and compared with IM (interval mapping).

<p>The horizontal bar represents genome wide significance at p = 0.05. <i>Mrip4</i> and <i>Mrip5</i> are confirmed as separate non-linked QTLs associated with adenoma multiplicity in the USI of the 2 Gy mice.</p

Main effect QTLs for tumour multiplicity in the small intestine of mice identified using a panel of 142 N2 irradiated (2Gy) mice.

<p>The chromosome (Chr.) and region defined as <i>Mrip (Mom</i> radiation-induced polyposis) are shown in column 1, with the traits; USI (upper small intestine) and LSI (lower small intestine) in column 2. The marker name and position are determined by MIT; (<a href="http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease" target="_blank">http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease</a>) and shown in column 3. Also given are the p-values with LRS (Likelihood Ratio Statistic), the percentage trait variance (%) and confidence intervals (CI). The level of significance for each association are categorised as suggestive (Su), significant (Si) or highly significant (HSi) based on LRS (value ≥ given in parenthesis).</p

Predictive assessment of <i>BALB</i> specific amino acid polymorphisms for potentially damaging alterations.

<p>We list the polymorphisms using MPD (Mouse Phenome Database) and known functional domains using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) within the <i>Mrip</i> regions. Polyphen predictions are based on position specific independent count (PSIC) and if >1.5 then potentially damaging and shown in bold. SIFT predicts the substitution to be tolerated (T) or not tolerated (N), if intolerant then the substitution effect is stated. The conservation of sequence alignment at and around the amino acid substitution is compared using EMBL-EBI.</p

Main effect QTLs for tumour multiplicity in the small intestine of mice identified using a panel of 112 N2 sham-irradiated mice.

<p>The first column shows the chromosome (Chr.) number with the traits; USI (upper small intestine) and LSI (lower small intestine) in column 2. The marker name and position (cM) are determined by MIT; (<a href="http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease" target="_blank">http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease</a>) and shown in column 3. Also given are the p-values with LRS (Likelihood Ratio Statistic), the percentage trait variance (%) and confidence intervals (CI). The level of significance attained was suggestive (Su) for all QTLS of the 0 Gy cohort.</p

A genome wide scan to show the LOD profiles of chromosomes 1–19 with adenoma multiplicity in the USI of the 2 Gy cohort.

<p>The horizontal line above the <i>y</i> axis represents a significant threshold score. Significant QTLs are detected on chromosomes 2, 5 and 16 and are defined as <i>Mom</i> radiation-induced polyposis (<i>Mrip</i>1–5; arrowed).</p

Summary of the process used in selecting genes from QTL regions.

<p>Summary of the process used in selecting genes from QTL regions.</p

The function of candidate genes and their role in radiation response and tumorigenesis.

<p>The function of candidate genes and their role in radiation response and tumorigenesis.</p

The LRS profile of <i>Mrip2</i> and <i>Mrip3</i> against markers distributed along chromosome 5 is determined using CIM (composite interval mapping) and compared with IM (interval mapping).

<p>The horizontal bar represents genome wide significance at p = 0.05. <i>Mrip2</i> and <i>Mrip3</i> are confirmed as separate non-linked QTLs associated with adenoma multiplicity in the USI of the 2 Gy mice.</p